The objective of the study is the characterization of the non-uniform geometry of a mountain river and the development of a method that identifies this geometry. Identification of the geometry enables simplification of a certain river section in modelling, which can be applied in a wide range of applications, for example the prediction of water levels. Identification is based on the tracer methodology, which means that a non-disintegrating substance is released upstream of a river reach and water levels and concentrations are continuously measured. Therefore attention has been paid to the flow and transport processes in a mountain stream with irregular geometry. The non-uniformity of the geometry of a mountain river affects the flow and transport processes. In the study the non-uniformity is modelled by the use of correction coefficients in the hydraulic model and the application of the stagnant zone concept in the transport model. The coefficients represent corrections for the influence of the non-uniformity of the depth and velocity profiles over the crosssection. The stagnant zone concept is based on the assumption of mass exchange between a zone with no net flow besides a main stream. A coupling can be found between the two concepts, which enables rewriting of the identified correction coefficients in a percentage of stagnant zones, relative to the total cross-section. Based on those principles, a flow and transport simulating numerical model is developed. The applicability of the identification system is limited to streams with moderate Froude numbers. The determination of the parameters in a system, in this study the geometrical and hydraulic coefficients, is an identification problem. Integration of the numerical model with the parameter identification procedure DUD results in a system that identifies a geometry for which the produced observations of water levels and concentrations coincide with the measurements. An additional result is the reconstruction of the upstream, unsteady, discharge.